DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Cytosine NucleotidesDNA-Cytosine Methylases: Methylases that are specific for CYTOSINE residues found on DNA.DNA (Cytosine-5-)-Methyltransferase: An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.5-Methylcytosine: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Cytosine Deaminase: An enzyme which catalyzes the deamination of CYTOSINE resulting in the formation of URACIL. It can also act on 5-methylcytosine to form THYMIDINE.Sulfites: Inorganic salts of sulfurous acid.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).DNA Modification Methylases: Enzymes that are part of the restriction-modification systems. They are responsible for producing a species-characteristic methylation pattern, on either adenine or cytosine residues, in a specific short base sequence in the host cell's own DNA. This methylated sequence will occur many times in the host-cell DNA and remain intact for the lifetime of the cell. Any DNA from another species which gains entry into a living cell and lacks the characteristic methylation pattern will be recognized by the restriction endonucleases of similar specificity and destroyed by cleavage. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms.Epigenomics: The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.Genomic Imprinting: The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Deamination: The removal of an amino group (NH2) from a chemical compound.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Methyltransferases: A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.Cytarabine: A pyrimidine nucleoside analog that is used mainly in the treatment of leukemia, especially acute non-lymphoblastic leukemia. Cytarabine is an antimetabolite antineoplastic agent that inhibits the synthesis of DNA. Its actions are specific for the S phase of the cell cycle. It also has antiviral and immunosuppressant properties. (From Martindale, The Extra Pharmacopoeia, 30th ed, p472)Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Flucytosine: A fluorinated cytosine analog that is used as an antifungal agent.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.S-Adenosylmethionine: Physiologic methyl radical donor involved in enzymatic transmethylation reactions and present in all living organisms. It possesses anti-inflammatory activity and has been used in treatment of chronic liver disease. (From Merck, 11th ed)Deoxyribonuclease HpaII: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.Nucleoside Deaminases: Catalyze the hydrolysis of nucleosides with the elimination of ammonia.GuanineHistone-Lysine N-Methyltransferase: An enzyme that catalyzes the methylation of the epsilon-amino group of lysine residues in proteins to yield epsilon mono-, di-, and trimethyllysine. EC 2.1.1.43.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.DNA, Neoplasm: DNA present in neoplastic tissue.UracilDinucleoside Phosphates: A group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Adenine NucleotidesCloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.RNA, Long Noncoding: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Cell Line, Tumor: A cell line derived from cultured tumor cells.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.ThymineLysine: An essential amino acid. It is often added to animal feed.Guanine NucleotidesDNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Site-Specific DNA-Methyltransferase (Adenine-Specific): An enzyme responsible for producing a species-characteristic methylation pattern on adenine residues in a specific short base sequence in the host cell DNA. The enzyme catalyzes the methylation of DNA adenine in the presence of S-adenosyl-L-methionine to form DNA containing 6-methylaminopurine and S-adenosyl-L-homocysteine. EC 2.1.1.72.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Protein Methyltransferases: Enzymes that catalyze the methylation of amino acids after their incorporation into a polypeptide chain. S-Adenosyl-L-methionine acts as the methylating agent. EC 2.1.1.Purine Nucleotides: Purines attached to a RIBOSE and a phosphate that can polymerize to form DNA and RNA.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Kinetics: The rate dynamics in chemical or physical systems.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Genes, p16: Tumor suppressor genes located on human chromosome 9 in the region 9p21. This gene is either deleted or mutated in a wide range of malignancies. (From Segen, Current Med Talk, 1995) Two alternatively spliced gene products are encoded by p16: CYCLIN-DEPENDENT KINASE INHIBITOR P16 and TUMOR SUPPRESSOR PROTEIN P14ARF.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Pyrimidine Nucleotides: Pyrimidines with a RIBOSE and phosphate attached that can polymerize to form DNA and RNA.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Genes, Tumor Suppressor: Genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check. When tumor suppressor genes are inactivated or lost, a barrier to normal proliferation is removed and unregulated growth is possible.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Genetic Variation: Genotypic differences observed among individuals in a population.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Antimetabolites, Antineoplastic: Antimetabolites that are useful in cancer chemotherapy.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Cytidine Deaminase: An enzyme that catalyzes the deamination of cytidine, forming uridine. EC 3.5.4.5.Hydroxamic Acids: A class of weak acids with the general formula R-CONHOH.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.Embryonic Stem Cells: Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Deoxycytosine Nucleotides: Cytosine nucleotides which contain deoxyribose as the sugar moiety.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Methyl-CpG-Binding Protein 2: A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.Prodrugs: A compound that, on administration, must undergo chemical conversion by metabolic processes before becoming the pharmacologically active drug for which it is a prodrug.Tumor Suppressor Proteins: Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.Death-Associated Protein Kinases: A family of calcium/calmodulin-dependent PROETIN-SERINE-THREONINE KINASES. They are ubiquitously expressed in adult and embryonic mammalian tissues, and their functions are tightly related to the early stages of eukaryotic programmed cell death.Chromatin Assembly and Disassembly: The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Insulin-Like Growth Factor II: A well-characterized neutral peptide believed to be secreted by the LIVER and to circulate in the BLOOD. It has growth-regulating, insulin-like and mitogenic activities. The growth factor has a major, but not absolute, dependence on SOMATOTROPIN. It is believed to be a major fetal growth factor in contrast to INSULIN-LIKE GROWTH FACTOR I, which is a major growth factor in adults.Uracil-DNA Glycosidase: An enzyme that catalyzes the HYDROLYSIS of the N-glycosidic bond between sugar phosphate backbone and URACIL residue during DNA synthesis.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Protein-Arginine N-Methyltransferases: Enzymes that catalyze the methylation of arginine residues of proteins to yield N-mono- and N,N-dimethylarginine. This enzyme is found in many organs, primarily brain and spleen.
Bisulfite sequencing
The nasal methylome as a biomarker of asthma and airway inflammation in children | Nature Communications
Metabolism, Part 2 - Exam #1 Flashcards by whitney miller | Brainscape
Patent US6960436 - Quantitative methylation detection in DNA samples - Google Patents
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Autosomal dominant cerebellar ataxia, deafness, and narcolepsy: MedlinePlus Genetics
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JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Lecture 32- Folate SUMMARY - /fi Nucleotide Felicficid BlosyntheSIS l J DHFR scrim TetrahydmfolatefiHF Methianinea S...
Frontiers | Enhancement of RNA-directed DNA methylation of a transgene by simultaneously downregulating a ROS1 ortholog using a...
How black truffles deal with the jumpers in th... ( The black truffle uses reversible ep...)
Methyltransferase and DNA - Stock Image - C015/5703 - Science Photo Library
Epigenetic changes don't last | Max-Planck-Gesellschaft
Technologies for Methylome Studies | Genome Canada
Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry | PNAS
Glossary
DNA Methylation
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression ...
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Epigenetics and Breast Cancers
Does Obesity Literally Accelerate Aging? - Fight Aging!
How Aging Is Recorded in Our Genes | WIREDCpG Islands Undermethylation in Human Genomic Regions under Selective Pressure
DNA Methylation and Its Effect on Various Cancers: An Overview | OMICS International
The MspJI family of modification-dependent restriction endonucleases for epigenetic studies | PNAS
Epigenetic Changes In Genomes Happen A Lot, But They Rarely Last | Science 2.0
GenesGuanineAdenineDinucleotidesTranscriptionalModificationMethyl cytosineQuantitativeProteinsAbstractChromatin structureHistonesPatterns of DNA methylationPromoter methylationGenomesHeritableSingle-nucleotide pEpigeneticsBisulfite treatmentGlobal DNA methylationBasesEmbryonic stemDNMTsStrandsAddition of a methyl groupGenome-wide DNA methylation patternsEpigenetic mechanismChanges in methylationTissuesAnalysis of allelic methylation statusEukaryoticPromotersTranscriptionLociReplicationGene expression and DNA methylationArabidopsisModifying DNA methylation patternsDifferential methylationEnzyme
Genes52
- As a result of these mutations, methylation is abnormal, which affects the expression of multiple genes. (medlineplus.gov)
- Researchers suggest that overexpression of the DNMT1 gene may result in methylation and silencing of genes called tumor suppressors. (medlineplus.gov)
- Recently, microRNAs have been found to regulate DNA methyltransferases (DNMTs) and thus control methylation status in several genes. (jove.com)
- De novo methylation of promoter Cpfi islands of tumor suppressor genes leading to gene inactivation 3. (coursehero.com)
- DNA methylation is a heritable epigenetic modification of the genes w. (bio-medicine.org)
- More than 58% of the 125 Mbp black truffle genome is made up of repetition and 'jumping genes' - sections of DNA which can move about within the genome. (bio-medicine.org)
- DNA methylation is a heritable epigenetic modification of the genes, where a methyl group is added to cytosine DNA nucleotides. (bio-medicine.org)
- While genes were disproportionately often affected, methylation of mobile DNA elements, transposons, was very stable. (mpg.de)
- This appears to make sense, since it was already known that artificially induced loss of methylation has a much greater effect on the activity of transposons than of regular genes. (mpg.de)
- It is now believed that tissue-specific expression is achieved by the epigenetic regulation of genes via processes such as DNA methylation. (genomecanada.ca)
- These aspects include the de novo discovery of differentially methylated genes, the analysis of methylation patterns, and the determination of differences in the degree of methylation. (pnas.org)
- We successfully applied this technology under high-throughput conditions to quantitatively assess methylation differences between normal and neoplastic lung cancer tissue samples from 48 patients in 47 genes and demonstrate that the quantitative methylation results allow accurate classification of samples according to their histopathology. (pnas.org)
- Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation") had even lower expression than genes with promoter methylation. (biomedcentral.com)
- Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. (biomedcentral.com)
- We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. (biomedcentral.com)
- Other enzymes are recruited to the region by ligand-ER α dimers which activate DNA demethylases to act simultaneously to increase gene expression of protooncogenes and growth-promoting genes. (hindawi.com)
- Epigenetic malfunctions are manifested through aberrant methylation and acetylation of genes and histones involved in normal tissue development to activate or silence gene expression. (hindawi.com)
- From a genetic point of view, there is a lot of truth in that statement: As we age, the core of our biological being - the sequence of our DNA, which makes up our genes - remains the same. (wired.com)
- Genes can be switched on and off as needed, and the regulation of genes often involves what are called epigenetic mechanisms in which chemical alterations are made to the DNA. (wired.com)
- In contrast, the small number of genes in the centenarian that had greater methylation levels were often those that needed to be kept turned on to protect against cancer. (wired.com)
- methylation is targeted to different genes in different cells during development and typically silences those genes, resulting in cell-type-specific gene expression. (krellinst.org)
- (1) studied DNA methylation in eight cancer-related genes in nasopharyngeal carcinoma. (aacrjournals.org)
- However, in small stretches of DNA termed CpG islands, which are ∼500 bp to 2000 bp in length (5) , the CpG dinucleotide occurs at near the expected frequency, and these areas are frequently located in and around the transcription start sites of approximately half of the human genes. (aacrjournals.org)
- Several tumor suppressor genes contain CpG islands in their promoters, and many of them show evidence of methylation silencing. (aacrjournals.org)
- Other genes frequently methylated in cancer are key players in cell cycle control ( p15 and p16 ) or are involved in DNA repair ( MGMT , hMLH1 , and GSTP1 ) and play important roles in protecting cells from carcinogenic agents. (aacrjournals.org)
- It has been notoriously difficult to accurately measure the level of methylation at given CpG sites within target areas of genes. (aacrjournals.org)
- One of the major hurdles in producing human clones, if it's possible, is the reprogramming of the human genome that's necessary to erasing most modifications that have been made in order to sequester or expose segments of DNA, thereby silencing or turning on different genes during the development and differentiation of various cells for different tissues. (reasons.org)
- DNA chains are double-stranded, antiparallel, complementary strings of nucleotides, abbreviated A, C, G, and T. The ordered sequence of nucleotides specifies genes, regulatory sequences, and other elements necessary for coordinated development and differentiation of cells and organisms. (reasons.org)
- Among 9 candidate genes, GNB4 was identified and validated by qRT-PCR as a potential target silenced by DNA methylation via DNA methyltransferase 3B (DNMT3B). (biomedcentral.com)
- Aberrant DNA methylation of cytosine nucleotides within the promoter region of tumor suppressor genes provides an epigenetic mechanism of transcriptional control associated with carcinogenesis. (aacrjournals.org)
- The results of further experiments suggested that reduced methylation at the four DNA regions prime the plant's immune system, enabling a faster and stronger activation of a multitude of defence genes across the genome after attack by downy mildew. (elifesciences.org)
- The next steps following on from this work are to investigate exactly how the four DNA regions with reduced methylation can prime so many different defence genes in the plant. (elifesciences.org)
- This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. (prolekare.cz)
- Most people have an understanding of genetics, that our outward characteristics are specified by genes encoded by the DNA sequence in our genome. (le.ac.uk)
- In reality, this means that there is another level of genetic control in addition to a person's DNA sequence which determines which genes are turned off and which are turned off. (le.ac.uk)
- The methylation patterns of specific genes are thought to be biomarkers for a variety of psychological disorders and may be the result of such factors such as childhood abuse, malnutrition, and traumatic stress. (tebu-bio.com)
- Remarkably, there was very little correlation between buccal and blood methylation patterns for 162 CpG sites studied from candidate genes implicated in genetic and epigenetic studies. (tebu-bio.com)
- Based on evolutionary presupposition, jumping genes were initially believed to be simply 'selfish' DNA with the sole function of self-perpetuation, and with no apparent use to the host (junk! (creation.com)
- Since DNA methylation (the linking of a methyl group to the nucleotide bases adenine or cytosine) 10 is important for switching off genes, it is believed that this process is also used by host cells to stop the movement of TEs. (creation.com)
- And this DNA methylation at cytosines is thought helps regulate genes try to help turn them on and off. (genome.gov)
- Additionally, the observed reduced CpG and increased TpG density at TSS of lowly expressed genes suggests DNA methylation plays a significant role in adaptive evolution through more permanent changes to lower gene expression. (biomedcentral.com)
- Folate metabolism is involved in synthesis, methylation and DNA repair, and several genes including methylenetetrahydrofolate reductase ( MTHFR ), methionine synthase ( MTR ) , reduced folate carrier 1 ( RFC1 ) and cystathionine β-synthase ( CßS ) regulate this metabolism. (termedia.pl)
- DNA hydroxymethylation, caused by oxidation of 5-methylcytosine through the TET family of enzymes, was further discovered to be involved in switching genes on and off. (biocat.com)
- There are two main mechanisms of epigenetically programming our DNA to silence or activate our genes. (dadamo.com)
- The second method in which the environment acts to control genes is through the addition or removal of acetyl groups from the proteins that the DNA strands wrap around, the histones. (dadamo.com)
- However, CGIs on the × chromosomes of females and those around imprinted genes are subject to monoallelic methylation in a random and a parent of origin-dependent manner, respectively [ 5 ]. (biomedcentral.com)
- It could also inform cancer research, as it could give scientists the opportunity to reactivate tumor suppressor genes that had been silenced by DNA methylation. (healthcanal.com)
- Points represent actual genes CG gene body methylation, gene expression, and their color represents their interaction sum on the same scale as the model colors. (nih.gov)
- DNA methylation, the chemical process that adds a methyl group to DNA, is the principal manner in which genes are transcriptionally repressed or silenced. (epigenie.com)
- H3K4 methylation is a marker for active genes, and there is an inverse correlation between the presence of trimethylated H3K4 and DNA methylation at promoters. (epigenie.com)
- Removal of H3K4 methylation by the histone demethylase LSD2 (KDM1B) is required for establishment of DNA methylation at the promoters of certain imprinted genes. (epigenie.com)
- But if you zoom in, there are a large number of short regions that show very tissue-specific DNA methylation, and the vast majority of these regions happened at the many regulatory elements encoded in the genome that control the genes specifically to a tissue. (ludwigcancerresearch.org)
Guanine10
- DNA contains the four bases thymine (T), cytosine (C), adenine (A) and guanine (G). These bases form base pairs along the length of the DNA helix. (genomebc.ca)
- CpG sites are DNA regions where a cytosine nucleotide occurs next to a guanine nucleotide. (pubmedcentralcanada.ca)
- MTT, apoptosis and cell cycle analyses were performed to examine the effect of either guanine nucleotide-binding protein beta-4 (GNB4) overexpression or knockdown on cell proliferation, apoptosis and cell cycle. (biomedcentral.com)
- Cytosine (C) is one of four chemical bases in DNA, the other three being adenine (A), guanine (G), and thymine (T). Within the DNA molecule, cytosine bases located on one strand form chemical bonds with guanine bases on the opposite strand. (genome.gov)
- Cytosine has the unique property in that it binds in the double helix opposite a guanine, one of the other nucleotides. (genome.gov)
- Vertebrate DNA methylation involves the addition of a methyl group to cytosine bases predominantly located 5' adjacent to a guanine (CpG sites) throughout the genome. (biomedcentral.com)
- CpG stands for Cytosine-phosphate-Guanine and is the most studied dinucleotide in mammalian genomes. (fmi.ch)
- In adult tissues, DNA methylation typically occurs in regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide, what geneticists call CpG Site. (dadamo.com)
- CHAPEL HILL, N.C. - For decades, scientists have known that DNA consists of four basic units - adenine, guanine, thymine and cytosine. (healthcanal.com)
- This modification occurs specifically at CpG sites, regions in which a cytosine nucleotide is located next to a guanine nucleotide that is linked by a phosphate ( Figure 1 ). (epigenie.com)
Adenine6
- Scientists have known for many years that an enzyme called Dam (DNA adenine methyltransferase) plays a role in regulating gene expression in many bacteria. (bio-medicine.org)
- In humans DNA methylation occurs on the C (cytosine) rather than the A (adenine) nucleotide. (bio-medicine.org)
- Two of DNA's four nucleotides, cytosine and adenine, can be methylated. (epigenomics.com)
- The recent identification of enzymes that make similar modifications to adenine bases (As) in messenger RNAs and in DNA is adding layers of complexity to the array of epigenetic signals that control development, differentiation, and adaptive changes of highly complex and dynamic cellular systems. (reasons.org)
- The m6A methyltransferases (N-6 adenine-specific DNA methylase) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. (wikipedia.org)
- But bacteria are often methylated at the nitrogen-6 position of adenine and the nitrogen-4 position of cytosine as well, and there have been no good techniques for locating these modifications in the genome. (the-scientist.com)
Dinucleotides7
- Cytosines in CpG dinucleotides can be methylated to form 5-methylcytosine. (pubmedcentralcanada.ca)
- Previously, methylation analysis relied on the use of methylation-sensitive restriction enzymes, which limited the number of CpG dinucleotides that could be assessed and was difficult in formalin-fixed material. (aacrjournals.org)
- CG dinucleotides enhance promoter activity independent of DNA methylation (2019). (fmi.ch)
- Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG. (biomedcentral.com)
- Most CpG dinucleotides in the mammalian genome are modified by a methyl group at the C5-position of the cytosine. (biomedcentral.com)
- CpG dinucleotides occur in mammalian genomes less frequently than would be expected from the GC-content of DNA, because methylated CpG frequently converts to TpG, while unmethylated CpG does not [ 2 ]. (biomedcentral.com)
- De novo DNA methylation at the cytosine in CpG dinucleotides is initiated by DNMT3A and DNMT3B. (epigenie.com)
Transcriptional8
- The conversion of cytosine to 5-methylcytosine in promoter-associated CpG islands can cause changes in chromatin structure and usually results in transcriptional silencing of the associated gene. (pnas.org)
- DNA methylation of non-coding region of DNA helps to maintain transcriptional silencing whereas in coding region of DNA it leads to an epigenetic modification. (omicsonline.org)
- This methylation of DNA not only causes change in transcriptional activity but also leads to change in chromatin structure in promoter region of the gene [ 5 ]. (omicsonline.org)
- The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. (prolekare.cz)
- Transcriptional Bypass of DNA-Protein and DNA-Peptide Conjugates by T7 RNA Polymerase. (nyu.edu)
- Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions.Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression.This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression. (nih.gov)
- Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions. (nih.gov)
- H3K9 methylation and DNA methylation are targeted via small interfering RNAs (siRNAs) to repeats and transposable elements (TEs) and are required for their transcriptional silencing , . (prolekare.cz)
Modification22
- In recent years it has become apparent that genetic information is stored not only in the arrangement of four nucleotide bases, but also in the covalent modification of selected bases. (pnas.org)
- In mammals, the main modification is methylation of cytosine. (pnas.org)
- DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. (biomedcentral.com)
- Cytosine DNA methylation is an epigenetic modification that is shared by many eukaryotic organisms. (biomedcentral.com)
- Altered DNA methylation patterns in coding strands lead to epigenetic modification. (omicsonline.org)
- All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N 12 /N 16 ) away from the modified cytosine. (pnas.org)
- A frequent epigenetic modification of DNA nucleotides involves the addition of a methyl group (-CH3) to cytosine bases (Cs). (reasons.org)
- DNA methylation, histone and chromatin modification, non-coding RNA deployment, RNA editing, and nuclear reorganization) and discuss the broad spectrum of epigenetic alterations that have been uncovered in pediatric and adult nervous system tumors. (mdpi.com)
- The central principle of ChIP is the use of an antibody targeting a protein or histone modification of interest to pull down DNA regions with which it associates. (abcam.com)
- ChIP can also be combined with epigenetic technologies such as bisulfite conversion to interrogate the interplay between histone modification and DNA methylation. (abcam.com)
- N 6 -methyladenine (6mdA) is a widespread DNA modification in bacteria. (sciencemag.org)
- The most common DNA modification in mammals is 5-methylcytosine (5mC), comprising ~3 to 6% of the total cytosines in human DNA ( 1 ). (sciencemag.org)
- 6mdA is a fundamental component of bacterial restriction-modification systems that allow prokaryotes to distinguish between benign host DNA and potentially pathogenic nonhost DNA ( 5 ). (sciencemag.org)
- Despite the lack of a known restriction-modification system in mammals, the presence of 6mdA has recently been reported in the DNA of mouse and human cells ( 4 , 6 - 10 ). (sciencemag.org)
- One such modification is to attach a tag, known as a methyl group, to a nucleotide base known as cytosine. (elifesciences.org)
- They repress transposable elements and maintain genome integrity though guiding DNA methylation and histone modification [ 9 - 11 ]. (pubmedcentralcanada.ca)
- Changes in gene expression arising from chemical modification of DNA or histone proteins. (le.ac.uk)
- These tails are largely unstructured and it is these that are the target for epigenetic modification including acetylation, methylation and phosphorylation. (le.ac.uk)
- We identify a motif strongly enriched in methylated/hydroxymethylated regions, and we propose that this motif recruits DNA modification machinery to specific chromosomes in the parental macronucleus. (biomedcentral.com)
- The most commonly studied type of eukaryotic modification, methylation of the carbon-5 position of cytosine, is relatively easy to identify through bisulfite sequencing. (the-scientist.com)
- 5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. (diagenode.com)
- Bisulfite modification of DNA is the most commonly used, " gold standard " method for DNA methylation studies providing single nucleotide resolution . (diagenode.com)
Methyl cytosine6
- Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq), we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. (biomedcentral.com)
- The methyl group adds to the 5' carbon of cytosine ring forming 5-methyl cytosine as shown in Figure 1 . (omicsonline.org)
- The stretch of DNA where there is frequent appearance of methyl cytosine is called CPG islands. (omicsonline.org)
- Global DNA Methylation Assay Kit (5 Methyl Cytosine, Colorimetric) (ab233486) contains all reagents necessary for the quantification of global DNA methylation. (abcam.com)
- McrBC specifically cleaves DNA containing methyl cytosine ( m C : 5-hydroxymethylcytosine, 5-methylcytosine, 4-methylcytosine) preceded by a purine nucleotide (Pu : A or G). DNA cleavage by McrBC requires at least two Pu m C sites within a distance of 40 - 2,000 bp. (clontech.com)
- Base excision repair mechanisms facilitate removal of methylation after deamination of methyl cytosine (5mC) creates a T:G mismatch. (epigenie.com)
Quantitative2
- Methylation through Fluorescence of a Single Strand (Methyl-FloSS) establishes a simple detection method for the quantitative analysis of methylation density. (aacrjournals.org)
- The intervention effect was evaluated by DNA methylation levels (quantitative real-time PCR assay) and anthropometric and biochemical variables (fasting plasma glucose, haemoglobin A1C, insulin, and vitamin E). (biomedcentral.com)
Proteins17
- These include determining whether the instructions in a particular segment of DNA are carried out or suppressed (gene silencing), regulating reactions involving proteins and fats (lipids), and controlling the processing of chemicals that relay signals in the nervous system (neurotransmitters). (medlineplus.gov)
- In vitro methylation assays, on the other hand, are useful biochemical assays, which are sensitive, and consistently reveal if the identified proteins are indeed PRMT substrates. (jove.com)
- The process where the initial strand of RNA copied directly from DNA is cut up (spliced) and pieced together into different messages (mRNAs) and can lead to different proteins from the same region of DNA. (genomebc.ca)
- a , Inside a cell nucleus, DNA is wrapped tightly around an octamer of highly basic histone proteins to form chromatin. (nih.gov)
- These changes affect how my DNA is read or expressed in different cells and which RNAs (both coding and noncoding) and proteins are made. (reasons.org)
- This is a dynamic process where DNA is compacted into chromatin fibres that associate with histone and non-histone proteins (Figure 1). (le.ac.uk)
- Histone proteins act like a spool that DNA can be wound around to become more compact. (le.ac.uk)
- Figure 2: DNA and histone proteins associated together using electrostatic interactions. (le.ac.uk)
- DNA (sugar-phosphate backbone: orange, bases: coloured lines) wraps around the histone proteins (coloured coils in centre) whose tails protrude from the structure and are modified. (le.ac.uk)
- Complex of DNA, histones, and non-histone proteins found in the nucleus of a eukaryotic cell. (nap.edu)
- As beta cells are killed by the immune system, fragments of beta cell-specific cell-free DNA and proteins are released into the periphery. (springer.com)
- The histones control whether the DNA is in a free, unwound form, ready to be read, or tightly wrapped up into chromatin, the packed mass of DNA and proteins in the nucleus. (dadamo.com)
- Translation Blockage: DNA is the template for the construction of proteins. (dadamo.com)
- These last two bases - called 5-formylcytosine and 5 carboxylcytosine - are actually versions of cytosine that have been modified by Tet proteins, molecular entities thought to play a role in DNA demethylation and stem cell reprogramming. (healthcanal.com)
- Last year, Zhang's group reported that Tet proteins can convert 5 methylC (the fifth base) to 5 hydroxymethylC (the sixth base) in the first of a four step reaction leading back to bare-boned cytosine. (healthcanal.com)
- Three families of proteins which bind methylated DNA have been identified so far. (epigenie.com)
- In mammals, DNA methylation is introduced by the DNMT1, DNMT3A, and DNMT3B enzymes, which are all large multi-domain proteins. (springer.com)
Abstract1
- abstract = "Cytosine methylation patterns are essential for the proper control of gene expression in higher vertebrates. (utmb.edu)
Chromatin structure5
- It is now widely accepted that there is a relationship between DNA methylation, chromatin structure, and human malignancies. (pnas.org)
- DNA methylation alters histones of chromatin structure by activating histone deacetylase (HDA). (omicsonline.org)
- 4 These epigenetic "markers" on DNA can be copied after DNA synthesis, resulting in heritable changes in chromatin structure. (aacrjournals.org)
- Epigenetic mechanisms are broadly defined as processes that regulate gene manifestation through the alteration of chromatin structure without changing nucleotide foundation Naproxen sodium sequences5,6. (biotuesday.ca)
- These heritable changes alter DNA accessibility and chromatin structure, thereby regulating patterns of gene expression. (epigenie.com)
Histones5
- HAD enzyme removes acetyl group from histone which allows stronger interaction between DNA backbone and histones. (omicsonline.org)
- So, in our little analogy, the wool yarn is the DNA, the cardboard that wraps the yarn into the skein, the histones. (dadamo.com)
- The histones start coiling up into chromatin, effectively silencing any further DNA reading. (dadamo.com)
- Histones are important for packing chromosomal DNA into nucleosomes and may be important regulators of cytosine methylation. (biology-online.org)
- It explained the natural, phisiological activity of endogenous enzymes not only upon DNA but also histones during vital developmental steps (cytodifferentiation, gametogenesis, embryogenesis, aging, stem cells capacity for tissue renewal etc). (slideshare.net)
Patterns of DNA methylation3
- However, the steady state levels and patterns of DNA methylation are maintained through the dynamic balance of DNA methylation and demethylation, and changing either side of the balance will certainly lead to the development of disease. (springer.com)
- Altered patterns of DNA methylation could also directly or indirectly alter gene expression and contribute to changes in synaptic strength that are thought to underlie the formation and maintenance of memories (center panel). (nih.gov)
- These lines share the same genetic background, but show variation in heritable patterns of DNA methylation. (elifesciences.org)
Promoter methylation7
- Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. (biomedcentral.com)
- Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. (biomedcentral.com)
- In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation. (biomedcentral.com)
- Bisulfite sequencing PCR (BSP) and gene sequencing were then performed to detect and analyze the correlation between PRKCZ gene promoter methylation and T2DM. (hindawi.com)
- (2) approaches the question of whether the presence of p16 promoter methylation in the sera of patients with colorectal cancer can be a useful marker for early detection and prognosis. (aacrjournals.org)
- Our results demonstrated a dose-dependent decrease in p15 INK4B promoter methylation density as measured by decreasing FDS, which is consistent with prior MSP analysis. (aacrjournals.org)
- Gene expression analyses revealed altered expression of the methionine adenosyltransferase Mat2a and BK channel subunit Kcnmb2 , which was associated with changes in Kcnmb2 promoter methylation in MD F1 mice. (nature.com)
Genomes6
- Over the last decade a series of new methods have been developed to investigate DNA methylation profiles across large DNA regions - chromosomes and even entire genomes. (genomecanada.ca)
- Finally, we will attempt to adapt the so-called deep sequencing for fine methylomic studies of complex genomes that should generate very detailed DNA methylation maps across a number of cells in one experiment. (genomecanada.ca)
- Levels of 5-mC are variable in animal genomes, ranging from undetectable amounts in some insects to about 2% of total DNA in vertebrates. (abcam.com)
- In addition to simply mapping the epigenomes of hundreds of bacteria species, including emerging pathogens, Roberts is adding to his library of knowledge on how bacteria use methylation to protect their genomes from the restriction enzymes they release to cut up invading viral DNA. (the-scientist.com)
- Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. (plantcell.org)
- Interestingly, increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs, implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. (plantcell.org)
Heritable1
- Patterns of plant DNA methylation in the plant genome can remain stable over multiple generations and influence heritable phenotypes ( Quadrana and Colot, 2016 ). (elifesciences.org)
Single-nucleotide p2
- This method is based on the single-strand conformation polymorphism analysis (SSCA) method developed for single-nucleotide polymorphism (SNP) analysis. (wikipedia.org)
- Large-scale single-nucleotide polymorphism (SNP) genotyping was hoped to reveal DNA variants that would explain much of the variance in complex phenotypes. (genetics.org)
Epigenetics2
- To get a better idea of how methylation patterns change with age, a team led by Manel Esteller, an epigenetics researcher at the Bellvitge Biomedical Research Institute in Barcelona, Spain, looked at two extreme cases: A newborn male baby and a man aged 103 years. (wired.com)
- In a new paper published online Sunday in Nature Genetics , first author Hon, senior author Bing Ren, PhD, Ludwig scientist at UC San Diego, and colleagues probe deeper into the mysteries of epigenetics, reporting on how DNA methylation changes in different kinds of tissue. (ludwigcancerresearch.org)
Bisulfite treatment5
- Bisulfite sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA to determine its pattern of methylation. (wikipedia.org)
- Methlylation specific PCR identifies nucleotide regions in which cytosines have been altered to uracils following bisulfite treatment of the DNA template. (clontech.com)
- Bisulfite treatment is considered the gold standard method for determining DNA methylation. (neb.com)
- Popular methods for analyzing DNA methylation on a gene-specific basis, after bisulfite treatment, include bisulfite sequencing, methylation specific PCR, and methylation-based microarrays. (biocat.com)
- Diagenode's Premium Bisulfite Kit rapidly converts DNA through bisulfite treatment. (diagenode.com)
Global DNA methylation1
- It has been well demonstrated that the decrease in global DNA methylation is one of the most important characteristics of cancer. (abcam.com)
Bases5
- In humans, approximately 1% of DNA bases undergo DNA methylation. (dadamo.com)
- Unlike adult cells, embryonic cells appear to have methylated cytosine bases all over the place. (dadamo.com)
- Now, with a finding published online in the July 21, 2011, issue of the journal Science , researchers from the UNC School of Medicine have discovered the seventh and eighth bases of DNA. (healthcanal.com)
- Because these bases represent an intermediate state in the demethylation process, they could be important for cell fate reprogramming and cancer, both of which involve DNA demethylation. (healthcanal.com)
- Once they realized the limitations of the assay, they redesigned it and were in fact able to detect the two newest bases of DNA. (healthcanal.com)
Embryonic stem1
- A few novel modified nucleotides, 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5carboxycytosine (5-caC), have been detected in human and mouse tissues as well as embryonic stem cells. (abcam.com)
DNMTs3
- c , Two types of DNMTs initiate DNA methylation. (nih.gov)
- De novo DNMTs methylate previously non-methylated cytosines, whereas maintenance DNMTs methylate hemi-methylated DNA at the complementary strand. (nih.gov)
- The various types of DNMTs are responsible for the maintenance and establishment of DNA methylation patterns. (biocat.com)
Strands13
- This is ascribed to the characteristic pH-induced conformational change of the DNA strands that leads to the different adsorption capability to the NPs surface, as demonstrated by pH-CD profiles of the respective DNA molecules. (jove.com)
- The pH-dependent catalysis of AuNPs is also encoded with structural information of the double-stranded DNA (including regulating strands and their complementary strands) that has conformation resistant or responsive to pH change. (jove.com)
- When the two parental DNA strands are separated in the S-phase of the mitosis, two hemimethylated strands are produced. (pubmedcentralcanada.ca)
- To detect this DNA methylation, the Johns Hopkins team found a way to single out the troublesome DNA strands that have a methyl group attached to them. (biologynews.net)
- Then, another lab process is used to make additional copies of the remaining target DNA strands that are linked to cancer. (biologynews.net)
- These partner molecules are attached to help researchers detect and count the DNA strands that are associated with cancer. (biologynews.net)
- To do this, these customized DNA strands are mixed with quantum dots, which are crystals of semiconductor material whose sizes are in the range of only few nanometers across. (biologynews.net)
- This behavior makes the cancer-related DNA strands light up and identify themselves. (biologynews.net)
- In the Johns Hopkins cancer test, the quantum dots have been coated with a chemical that is attracted to biotin-one of the two molecules that were attached to the DNA strands. (biologynews.net)
- As a result, up to 60 of the targeted DNA strands can stick themselves to a single quantum dot, like arms extending from an octopus. (biologynews.net)
- The quantum dots grab this energy and immediately transfer it to the fluorescent dyes that were attached earlier to the targeted DNA strands. (biologynews.net)
- Although columns of this type typically remove DNA fragments greater than around 10 kb, the vast majority of strands produced by bead beating with the OmniLyse fall below this size limit and are retained in the eluate. (nanoporetech.com)
- After replication, DNMT1 maintains the methylation state in the daughter strands. (epigenie.com)
Addition of a methyl group1
- DNA methylation, the most well-studied type of epigenetic variation, comprises the addition of a methyl group (CH3) to cytosine. (europa.eu)
Genome-wide DNA methylation patterns1
- The new work is the first to compare the complete, genome-wide DNA methylation patterns of these two diverse age groups, says Martin Widschwendter, an oncologist at University College London in the United Kingdom who has studied the link between methylation and cancer. (wired.com)
Epigenetic mechanism1
- The covalent attachment of methyl groups to nucleotides, DNA methylation, is a key epigenetic mechanism in mammals. (sciencemag.org)
Changes in methylation3
- Alternatively, changes in methylation status within a cell may act to render it aplastic, in effect stabilizing the current synaptic weights and responsivity (right panel). (nih.gov)
- They used weighted gene comethylation network analysis (WGCNA) to spot changes in methylation patterns linked to ART initiation. (natap.org)
- Although we examined the methylation levels of 43,840 CpG sites in the control and BPA (200 μg/kg/day)-treated group (6 mice per group), we found no statistically significant changes in methylation levels in any CpG sites. (deepdyve.com)
Tissues13
- Ehrlich M, Gama-Sosa MA, Huang LH et al (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. (springer.com)
- However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. (biomedcentral.com)
- Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. (biomedcentral.com)
- Methylation patterns vary among major classes of cells in the brain and across cell samples from different tissues and organs. (krellinst.org)
- Thus, before DNA methylation can broadly be used for early detection, it will be necessary to show which DNA methylation patterns in normal-appearing tissues are associated with carcinogenesis and which DNA methylation patterns are associated with age but do not predispose to cancer in general. (aacrjournals.org)
- Notably the authors demonstrate that buccal DNA contains enrichment of these hypomethylated tDMRs (hypo-tDMRs) near disease associated single nucleotide polymorphisms (SNPs) and that buccal DNA shows a signfiicantly greater agreement with methylation patterns in other tissues: skeletal muscle, islets, brain, and liver. (tebu-bio.com)
- These buccal cell DNA collection kits are expected to help researchers collect surrogate DNA for a variety of tissues in addition to brain. (tebu-bio.com)
- Blood will likely remain the sample of choice for epigenomic studies of blood-related disease, and for certain tissues, buccal cell DNA was always the most logical choice. (tebu-bio.com)
- 1%) was also detected in all non-neuronal somatic tissues, with differences in tissue clustering observed based on CpG and non-CpG methylation patterns. (biomedcentral.com)
- 3. Horvath S. DNA methylation age of human tissues and cell types. (natap.org)
- We created very high resolution maps of DNA methylation for 17 diverse tissues in an individual mouse," said Hon. "Interestingly, we found that if you look at DNA methylation with a wide angle lens, you'll find that it is generally constant between different tissues. (ludwigcancerresearch.org)
- Ren, Hon and colleagues discovered, to their surprise, that in adult tissues, some of these regions of tissue-specific DNA methylation involved regulatory elements that were no longer active, but had been during development. (ludwigcancerresearch.org)
- They simply help understanding of development," said Hon. But they may also auger greater import in the future, bolstering the recognized importance of DNA methylation and providing "an epigenetic signature that can be used to find regulatory elements active in development, but which are no longer active in adult tissues. (ludwigcancerresearch.org)
Analysis of allelic methylation status2
- HM-WGA-PCR would serve as a reliable alternative to HM-PCR in the analysis of allelic methylation status when the quantity of DNA available is limited. (biomedcentral.com)
- Accordingly, HM-PCR is not suitable for a comprehensive analysis of allelic methylation status when the quantity of sample DNA is limited. (biomedcentral.com)
Eukaryotic3
- Eukaryotic cytosine methylation plays an important role in the regulation of gene expression and genome stability. (elifesciences.org)
- DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. (biomedcentral.com)
- For bacterial species identification, the 16S ribosomal RNA gene can be amplified from all bacteria non-specifically, without amplifying eukaryotic host DNA, or viruses. (nanoporetech.com)
Promoters3
- Dr Pao-Yang Chen, from UCLA says: "Instead of the methylated gene body or promoters that we usually see in plants and animals, the black truffle has very little gene body methylation and it appears that the methylation is occurring in the transposon. (bio-medicine.org)
- Genome arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed a globally hypermethylated crown gall genome, while promoters were rather hypomethylated. (prolekare.cz)
- Thus, it is important to profile DNA methylation at human gene promoters in each type of adult tissue and during different stages of human development [ 7 ]. (biomedcentral.com)
Transcription10
- An interplay between the above, as well as basic cell processes, such as transcription regulation, DNA replication, cell cycle regulation and DNA repair therefore determine the accuracy and function of neuronal connections. (frontiersin.org)
- The relationship between gene body methylation and transcription is currently not well understood. (biomedcentral.com)
- When located in a gene promoter, DNA methylation typically acts to repress gene transcription. (epigenomics.com)
- These methyl groups project into major groove of DNA, which in turn inhibit transcription [ 1 ]. (omicsonline.org)
- ChIP-loop is ideally suited to examine DNA loops mediated by transcription factor is a master regulator of chromatin-loop structure at the Kcnq5 locus. (abcam.com)
- Analysis of over 500,000 CpG sites demonstrated genome wide methylation patterns similar to those observed in humans, including reduced methylation within CpG islands and at transcription start sites (TSS), X chromosome inactivation, and anticorrelation of TSS CpG methylation with gene expression. (biomedcentral.com)
- This study provides baseline methylation and gene transcription profiles for a healthy adult pig, reports similar patterns to those observed in humans, and supports future porcine studies related to human disease and development. (biomedcentral.com)
- 5-Formylcytosine-induced DNA-peptide cross-links reduce transcription efficiency, but do not cause transcription errors in human cells. (nyu.edu)
- Inserting methyl groups changes the appearance and structure of DNA, which may directly block DNA recognition and binding of transcription factors, or may attract other factors that preferentially bind to DNA to interfere with transcription factor accessibility. (epigenie.com)
- DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. (prolekare.cz)
Loci4
- Other non-sequencing strategies are also employed to interrogate the methylation at specific loci or at a genome-wide level. (wikipedia.org)
- Methylation patterns can be characterized by interrogating specific loci or through genome-wide methylation profiling. (neb.com)
- Here, we showed a high cytosine DNA methylation status at ta-siRNA -generating loci in Arabidopsis ( Arabidopsis thaliana ), which is dependent on RDR6, SGS3, and DNA-DIRECTED RNA POLYMERASE V (PolV). (plantphysiol.org)
- In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. (prolekare.cz)
Replication1
- Methylation is a biological process used to tag a variety of molecules, including DNA, and is important in cellular processes such as regulating gene expression, DNA replication and repair. (bio-medicine.org)
Gene expression and DNA methylation2
- The whole-genome gene expression and DNA methylation profilings were performed using fulvestrant-resistant cell line 182 R -6 and tamoxifen-resistant cell line TAM R -1 as a model system. (biomedcentral.com)
- Based on comparisons of global gene expression and DNA methylation between the wild-type and resistant epiRILs, we discuss mechanisms by which the pericentromeric epiQTLs could regulate the defence-related transcriptome. (elifesciences.org)
Arabidopsis5
- A DNA glycosylase REPRESSOR OF SILENCING 1 (ROS1) participates in DNA demethylation in Arabidopsis and may possibly counteract RdDM. (frontiersin.org)
- To determine the rate and distribution of methylation changes in the genome, the German biologists looked at ten Arabidopsis lines. (mpg.de)
- studied how DNA methylation in a small weed known as Arabidopsis thaliana affects how well the plants can resist a disease known as downy mildew. (elifesciences.org)
- In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. (prolekare.cz)
- To investigate whether DNA methylation plays a role in heterosis, we compared at single-base-pair resolution the DNA methylomes of Arabidopsis thaliana Landsberg erecta and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis. (plantcell.org)
Modifying DNA methylation patterns1
- Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. (springer.com)
Differential methylation1
- This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression. (nih.gov)
Enzyme12
- This enzyme is involved in DNA methylation, which is the addition of methyl groups, consisting of one carbon atom and three hydrogen atoms, to DNA molecules. (medlineplus.gov)
- In particular, the enzyme helps add methyl groups to DNA building blocks (nucleotides) called cytosines. (medlineplus.gov)
- Scientists have known for many years that an enzyme called Dam (DNA ad. (bio-medicine.org)
- Using the X-ray diffraction facility at the Argonne National Laboratory in Chicago, Xiaodong Cheng, PhD, professor of biochemistry at Emory University School of Medicine and Georgia Research Alliance Eminent Scholar, and John Horton, PhD, Research Assistant Professor, have now solved the co-crystal structure of the Dam enzyme in complex with DNA, which has allowed them to observe exactly how the enzyme finds its target on bacterial DNA. (bio-medicine.org)
- Retroelement jumping involves copying its RNA transcript back into DNA (see figure) using the enzyme reverse transcriptase. (creation.com)
- The MTHFR enzyme, encoded by the MTHFR gene, is responsible for the catalysis of the irreversible reaction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate , which interferes in DNA synthesis and methylation. (termedia.pl)
- This methylation-laying enzyme resulted in a complete epigenetic makeover, the team learned . (the-scientist.com)
- On the other hand, when DNA is acted upon by an enzyme called histone deacetylase, it starts pulling acetyl groups off the histone. (dadamo.com)
- Each lot of every DNA restriction enzyme undergoes stringent quality control tests. (clontech.com)
- Takara Bio DNA restriction enzymes are supplied with optimized buffers that provide maximum activity during restriction enzyme digestion. (clontech.com)
- Visit our Restriction Enzyme Applications pages for information on how to digest DNA, relative activity in each Universal Buffer, star activity, buffers for double digestion, effects of DNA methylation, how to inactivate enzymes, and more. (clontech.com)
- Each lot of every enzyme undergoes four quality tests including: overdigestion, Genome DNA analysis, Ligation-Recutting and pKF3 Cloning. (clontech.com)
